Merge pull request #324 from Bonder-MJ/master

Small stuff
Merge pull request #325 from Bonder-MJ/master

Pom update
Merge pull request #326 from Bonder-MJ/master

commandline fix
Merge pull request #327 from Bonder-MJ/master

Updates
Code refactoring

Moved code from Main.java to the proper classes
Added objects to the calculator. Each calculator consists of one
phenotype and contains the risk snps with risk alleles.
Merge pull request #328 from rudi2013/master

Code refactoring
Merge branch 'master' of https://github.com/molgenis/systemsgenetics